Reordering frames according to gmx cluster monte-carlo method results

User discussions
1

GROMACS version: 2020.4
GROMACS modification: No
Hello,
gmx cluster explains that “reorder the RMSD matrix using Monte Carlo such that the order of the frames is using the smallest possible increments. With this it is possible to make a smooth animation going from one structure to another with the largest possible (e.g.) RMSD between them, however the intermediate steps should be as small as possible.”
I was wondering, after obtaining the reordered RMSD matrix, what is the way to go to create this smooth animation?

Thank you in advance,

Agustin Zavala

2

Hi,
I have never performed this analysis. Thus I hope others have a more accurate answer than mine.
But I guess the next step is to visualize the structures is to prepare the corresponding traj file, Maybe the option -cl save the re-order frames.
To better visualize the matrix you can convert xpm format in ps (using xpm2ps) gmx xpm2ps — GROMACS 2021.2 documentation
\Alessandra

3

I’ll try that, see if it works. Thanks!